LAMMPS (4 Nov 2022)
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain

units real

boundary p p p

atom_style full

pair_style lj/class2/coul/cut 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

variable T equal 530

read_data trimer.data   extra/bond/per/atom 5   extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-200 -200 -200) to (200 200 200)
  1 by 1 by 1 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  48 atoms
  scanning bonds ...
  8 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  33 = max dihedrals/atom
  scanning impropers ...
  26 = max impropers/atom
  reading bonds ...
  50 bonds
  reading angles ...
  84 angles
  reading dihedrals ...
  127 dihedrals
  reading impropers ...
  20 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     8 = max # of 1-3 neighbors
    17 = max # of 1-4 neighbors
    46 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

molecule mol1 grow_styrene_pre.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  30 atoms with max type 4
  31 bonds with max type 6
  51 angles with max type 10
  73 dihedrals with max type 13
  13 impropers with max type 3
molecule mol2 grow_styrene_post.molecule_template
Read molecule template mol2:
  1 molecules
  1 fragments
  46 atoms with max type 4
  48 bonds with max type 6
  81 angles with max type 10
  121 dihedrals with max type 13
  19 impropers with max type 3

fix myrxns all bond/react stabilization yes statted_grp .03     react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map         modify_create fit create_fit overlap 2.0         stabilize_steps 200 max_rxn 30
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100

fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1

thermo_style custom step temp press density f_myrxns[1]

thermo 100

dump 1 all xyz 1 test_vis.xyz

run 8000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 77 77 77
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 36.99 | 36.99 | 36.99 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]  
         0   0              0.076588866    8.1070333e-06  0            
       100   598.41967     -0.1670029      1.0809378e-05  1            
       200   696.77845      0.11857422     1.0809378e-05  1            
       300   932.97222     -0.058615676    1.3511722e-05  2            
       400   1016.3732      0.062233715    1.3511722e-05  2            
       500   1006.451      -0.17987841     1.6214067e-05  3            
       600   1143.8859      0.33297898     1.6214067e-05  3            
       700   1209.6144     -0.22743773     1.8916411e-05  4            
       800   1429.1639      0.14048255     1.8916411e-05  4            
       900   1375.0968     -0.04016551     2.1618755e-05  5            
      1000   1583.6696     -0.23364852     2.1618755e-05  5            
      1100   1811.0697     -0.054436797    2.43211e-05    6            
      1200   1928.4658      0.012242837    2.43211e-05    6            
      1300   1666.6176      0.057157656    2.43211e-05    6            
      1400   1686.18       -28.442814      2.7023444e-05  7            
      1500   1704.6248     -0.16861218     2.7023444e-05  7            
      1600   2171.7628     -33.6156        2.9725789e-05  8            
      1700   1991.2922     -0.11813381     2.9725789e-05  8            
      1800   2037.4991     -40.015612      3.2428133e-05  9            
      1900   2143.9447     -0.090964375    3.2428133e-05  9            
      2000   1927.9564      0.29856007     3.2428133e-05  9            
      2100   2255.5877     -4.9166327      3.5130478e-05  10           
      2200   2512.5193      0.00044804842  3.5130478e-05  10           
      2300   2336.1503     -45.094726      3.7832822e-05  11           
      2400   2508.9655     -0.1024684      3.7832822e-05  11           
      2500   2747.7344     -53.939212      4.0535167e-05  12           
      2600   2790.5736      0.07042181     4.0535167e-05  12           
      2700   3014.7092     -0.0025387793   4.0535167e-05  12           
      2800   2745.0295     -0.099361314    4.3237511e-05  13           
      2900   2952.1281     -0.13667582     4.3237511e-05  13           
      3000   3032.5298      0.28882784     4.5939855e-05  14           
      3100   3149.992       0.55269076     4.5939855e-05  14           
      3200   3422.5233     -0.11794908     4.86422e-05    15           
      3300   3040.2691     -0.067532834    4.86422e-05    15           
      3400   3323.3263      0.049969149    5.1344544e-05  16           
      3500   3539.0877     -0.065546641    5.1344544e-05  16           
      3600   3894.6897     -0.24222461     5.4046889e-05  17           
      3700   3689.3513      0.21366533     5.4046889e-05  17           
      3800   3924.799      -0.60817646     5.6749233e-05  18           
      3900   3713.1947     -0.024834682    5.6749233e-05  18           
      4000   3887.6151      0.052787631    5.9451578e-05  19           
      4100   3868.2877      0.42532898     5.9451578e-05  19           
      4200   3784.9874     -0.12018512     5.9451578e-05  19           
      4300   4169.9997      0.19652089     6.2153922e-05  20           
      4400   4112.291      -0.084839982    6.2153922e-05  20           
      4500   3974.2226     -0.13641761     6.2153922e-05  20           
      4600   4064.3852      0.16435039     6.2153922e-05  20           
      4700   3880.0044     -0.42874552     6.2153922e-05  20           
      4800   4508.2324      0.20208091     6.2153922e-05  20           
      4900   4364.033      -0.56300441     6.2153922e-05  20           
      5000   4030.4642     -0.29006515     6.2153922e-05  20           
      5100   4010.9518      0.32060145     6.2153922e-05  20           
      5200   4058.5072      0.088924924    6.2153922e-05  20           
      5300   4529.9866     -0.38882748     6.4856266e-05  21           
      5400   4305.9161      0.24046553     6.4856266e-05  21           
      5500   4556.8628     -0.014044879    6.4856266e-05  21           
      5600   4730.2206      0.1526293      6.4856266e-05  21           
      5700   4810.9968     -17.600253      6.7558611e-05  22           
      5800   4655.651      -0.25941928     6.7558611e-05  22           
      5900   4507.1045     -0.084691005    6.7558611e-05  22           
      6000   4516.0965      0.092662842    7.0260955e-05  23           
      6100   4592.4068      0.10403004     7.0260955e-05  23           
      6200   4583.9491      0.1692786      7.29633e-05    24           
      6300   4512.226       0.32590723     7.29633e-05    24           
      6400   4885.9205     -0.24208842     7.5665644e-05  25           
      6500   5250.5008      0.4135064      7.5665644e-05  25           
      6600   5216.9452      0.00059199905  7.8367989e-05  26           
      6700   5302.2925      0.50452368     7.8367989e-05  26           
      6800   4931.7328     -0.064719953    8.1070333e-05  27           
      6900   5549.8746      0.55101191     8.1070333e-05  27           
      7000   5472.9107      0.31358281     8.3772677e-05  28           
      7100   5559.9339      0.14034743     8.3772677e-05  28           
      7200   5726.4492     -0.39732059     8.6475022e-05  29           
      7300   5869.324       0.18989804     8.6475022e-05  29           
      7400   6109.5519      0.11206572     8.9177366e-05  30           
      7500   5966.7085      0.2059557      8.9177366e-05  30           
      7600   6051.2064      0.025316679    8.9177366e-05  30           
      7700   5719.6669      0.16548544     8.9177366e-05  30           
      7800   6118.8183     -0.20036999     8.9177366e-05  30           
      7900   6477.1901      0.10308473     8.9177366e-05  30           
      8000   6241.9498      0.090165102    8.9177366e-05  30           
Loop time of 17.4848 on 1 procs for 8000 steps with 528 atoms

Performance: 39.531 ns/day, 0.607 hours/ns, 457.540 timesteps/s, 241.581 katom-step/s
97.6% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.0991     | 3.0991     | 3.0991     |   0.0 | 17.72
Bond    | 7.6807     | 7.6807     | 7.6807     |   0.0 | 43.93
Neigh   | 1.6906     | 1.6906     | 1.6906     |   0.0 |  9.67
Comm    | 0.019091   | 0.019091   | 0.019091   |   0.0 |  0.11
Output  | 4.5095     | 4.5095     | 4.5095     |   0.0 | 25.79
Modify  | 0.46277    | 0.46277    | 0.46277    |   0.0 |  2.65
Other   |            | 0.02296    |            |       |  0.13

Nlocal:            528 ave         528 max         528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          35904 ave       35904 max       35904 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 35904
Ave neighs/atom = 68
Ave special neighs/atom = 11.409091
Neighbor list builds = 1836
Dangerous builds = 0

# write_data final.data nofix
Total wall time: 0:00:17
